Datasets were searched for using the same filters as before - must be human tissue that expressed lewy bodies, must have at least 3 patients and 3 controls, and must…
10 datasets were identified:
| CodeID | Tissue/Cell type | Variant | Samples | Type of array | GEO Ref | Comments | PIs |
|---|---|---|---|---|---|---|---|
| DIJ | Substantia Nigra | not specified | 15 disease, 8 control | Affymetrix Human Genome U133 Plus 2.0 Array | GSE49036 | Has some Braak staging | Dijkstra AA, Ingrassia AI, de Menezes RX, van Kesteren RE, Rozemuller AM, Heutink P, vandeBerg WJ |
| FFR | Substantia Nigra | not specified | 9 replicates for the controls and 16 replicates for the Parkinson’s disease patients | Affymetrix Human Genome U133 Plus 2.0 Array | GSE7621 | Ffrench-Mullen JM | |
| MOR.SN | Substantia nigra, split into medial and lateral portions | sporadic | 15 samples of medial parkinsonian SN, 9 samples of lateral parkinsonian SN (24), 8 medial nigra control samples and 7 lateral nigra control samples(15) | Affymetrix Human Genome U133A Array | GSE8397 | Age and sex | Moran LB, Graeber MB |
| MID1 | Substantia Nigra pars compacta | not specified | 10 PD brain samples and 8 control | Affymetrix Human Genome U133 Plus 2.0 Array | GSE20141 | Middleton FA, Kim PD, Zhang-James Y, Davis RL | |
| MID2 | Whole substantia nigra | not specified | 18 controls, 11 patients | Affymetrix Human Genome U133A Array | GSE20292 | Age and sex | Middleton FA, James M, Zhang Y, Davis RL |
| DUM | Cortex (BA9) | not specified | 29 PD, 44 neurologically normal controls | Illumina HiSeq 2000 | GSE68719 | Have age of death, sex, and some samples have corresponding proteomics | Dumitriu A, Golji J, Labadorf AT, Gao B, Beach TG, Myers RH, Longo KA, Latourelle JC |
| MOR.FC | Frontal cortex | sporadic | 3 Controls 5 Patients | Affymetrix Human Genome U133A Array | GSE8397 | Age and sex | Moran LB, Graeber MB |
| LEW | Dorsal Nucleus of the Vagus Nerve | not specified | 6 PD samples and 4 controls | Affymetrix Human Genome U133A 2.0 Array | GSE19587 | Age and sex | lewandowski nm, small sa |
| MID3 | Prefrontal cortex | not specified | 15 controls 14 patients | Affymetrix Human Genome U133A Array | GSE20168 | Age and sex | Middleton FA, James M, Zhang Y, Davis RL |
| MID4 | Putamen | not specified | 20 controls and 15 patients | Affymetrix Human Genome U133A Array | GSE20291 | Age and sex | Middleton FA, James M, Zhang Y, Davis RL |
| BOT1 | Locus Coeruleus | LRRK2 | 4 controls and 2 patients | Affymetrix Human Exon 1.0 ST Array | GSE34516 | LC does degenerate in PD. Main source of noradrenaline. | Botta-Orfila T, Sánchez-Pla A, Fernández M, Carmona F, Ezquerra M, Tolosa E |
| BOT2 | Putamen | LRRK2 | 5 controls and 3 patients | Affymetrix Human Exon 1.0 ST Array | GSE23290 | NA | Botta-Orfila T, Tolosa E, Gelpi E, Sànchez-Pla A, Martí M, Valldeoriola F, Fernández M, Carmona F, Ezquerra M |
Checked data distribution using PCA and boxplots. Some of the datasets have quite mixed samples wereas others separate quite nicely into controls and patients. Boxplots didn’t suggest any samples were outliers.